BAMInFormatter

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
val companion: BAMInFormatter.type

Attributes
protected
Definition Classes
BAMInFormatter → InFormatter
val converter: AlignmentRecordConverter

A converter from AlignmentRecord to SAMRecord.
A converter from AlignmentRecord to SAMRecord.

Definition Classes
BAMInFormatter → AnySAMInFormatter
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
val header: SAMFileHeaderWritable

A serializable form of the SAM File Header.
A serializable form of the SAM File Header.

Definition Classes
BAMInFormatter → AnySAMInFormatter
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def makeWriter(os: OutputStream): SAMFileWriter

Attributes
protected
Definition Classes
BAMInFormatter → AnySAMInFormatter
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val recordGroups: RecordGroupDictionary

A dictionary describing the read groups these reads are from.
A dictionary describing the read groups these reads are from.

Definition Classes
BAMInFormatter → AnySAMInFormatter
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
def write(os: OutputStream, iter: Iterator[AlignmentRecord]): Unit

Writes alignment records to an output stream in SAM format.
Writes alignment records to an output stream in SAM format.
os
An OutputStream connected to a process we are piping to.
iter
An iterator of records to write.

Definition Classes
AnySAMInFormatter → InFormatter

Related Docs: object BAMInFormatter | package read

case class BAMInFormatter extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val companion: BAMInFormatter.type

val converter: AlignmentRecordConverter

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

val header: SAMFileHeaderWritable

final def isInstanceOf[T0]: Boolean

def makeWriter(os: OutputStream): SAMFileWriter

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val recordGroups: RecordGroupDictionary

final def synchronized[T0](arg0: ⇒ T0): T0

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

def write(os: OutputStream, iter: Iterator[AlignmentRecord]): Unit

Inherited from Product

Inherited from Equals

Inherited from AnySAMInFormatter[BAMInFormatter]

Inherited from InFormatter[AlignmentRecord, AlignmentRecordRDD, BAMInFormatter]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped